BlueBrain atlas-densities issues

BlueBrain / atlas-densities

Tools to compute densities in the context of brain atlases.

Apache License 2.0

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issues

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Missing data for some brain regions in visual area

#83 gaole2019 opened 1 month ago
3
Quell warnings with new versions of pandas

#82 mgeplf closed 1 month ago
0
Updating regression requirements

#81 mgeplf closed 2 weeks ago
1
Fix nans in `compute_region_volumes`

#80 mgeplf closed 1 month ago
0
Speedup mtype density creation from probability maps using voxcell's ValueToIndexVoxels

#79 eleftherioszisis closed 2 months ago
2
Cleanup app tests

#78 mgeplf closed 3 months ago
1
Use voxel index to speed up the computation of densities

#77 eleftherioszisis closed 3 months ago
1
indent Test_mtype_densities_from_composition test right

#76 mgeplf closed 3 months ago
1
Fix fitting and optimization steps

#75 drodarie closed 3 months ago
4
Add check to the region filter in case the input dataset is all equal to 0 for the region of interest.

#74 drodarie closed 3 months ago
1
Faster compute average intensities

#73 mgeplf closed 3 months ago
1
Faster _compute_region_cell_counts

#72 mgeplf closed 3 months ago
1
Cleanup

#71 mgeplf closed 3 months ago
1
allow skipping normalization when `compute_cell_density`

#70 mgeplf closed 3 months ago
9
Is `atlas_densities/app/data/metadata/thalamus_metadata.json` actually used?

#69 asoplata opened 4 months ago
1
Add r_square values to the results of the fitting.

#68 drodarie closed 4 months ago
0
Remove need for config file for `atlas-densities cell-densities fit-average-densities command

#67 mgeplf opened 4 months ago
9
Hard-coded CCFv2 slice numbers for gene markers should be removed and set as an input parameter

#66 Sebastien-PILUSO opened 4 months ago
6
Feature/improve region counting

#65 drodarie opened 4 months ago
1
Lookup table for literature integration and fitting

#64 drodarie opened 4 months ago
3
remove pkg_resources, use importlib

#62 mgeplf closed 5 months ago
0
Drop literature values from regions that are not in hierarchy or not in the annotation volume

#61 drodarie closed 5 months ago
5
Exception in fitting due to regions in json hierarchy but not in the annotations volume

#60 drodarie closed 5 months ago
7
add `atlas-densities combination manipulate`

#59 mgeplf closed 5 months ago
2
Missing input gene volumes

#58 francesshei opened 5 months ago
4
Hard coded E-type in scale_excitatory_densities

#57 KeremKurban closed 3 months ago
8
fix documentation building

#56 mgeplf closed 5 months ago
1
Configurable group ids region names

#55 mgeplf closed 7 months ago
8
WIP: Config super region names

#54 mgeplf closed 9 months ago
0
put functions that are in densities.utils in the module that uses the…

#53 mgeplf closed 9 months ago
1
filter some warnings

#52 mgeplf closed 9 months ago
0
Update utils.py

#51 Sebastien-PILUSO closed 7 months ago
15
Allow specifying the "root" name

#50 mgeplf closed 9 months ago
2
split probability_map.csv into isocortex layers

#49 mgeplf closed 6 months ago
2
Leaf region will only trigger if the region exists

#48 cveraszto opened 10 months ago
2
update readme, make sure required joblib version is set

#47 mgeplf closed 10 months ago
0
add --region-name as an option to inhibitory-neuron-densities

#46 mgeplf closed 10 months ago
0
add `--region-name` as an option to `fit-average-densities`

#45 mgeplf closed 10 months ago
9
Nsetm 2196 expand output

#44 edasubert opened 11 months ago
0
Nsetm 2196 synapse class

#43 edasubert closed 10 months ago
2
Switch from attribute 'name' to 'acronym'

#42 lecriste closed 10 months ago
1
Nsetm 2196 update output

#41 edasubert closed 11 months ago
5
Nsetm 2196 multiple probability maps

#40 edasubert closed 11 months ago
1
Parallel

#39 edasubert closed 11 months ago
1
Stop using as many config files

#38 edasubert closed 11 months ago
14
speed up density creation

#37 edasubert closed 11 months ago
1
Csv update

#36 dkeller9 closed 5 months ago
5
L3_TPC:B type label should be replaced with L3_TPC:C

#35 crisely09 closed 8 months ago
16
Nsetm 2196 update the probability map

#34 edasubert closed 11 months ago
1